Merge branch 'topic/default/update-doc' into 'branch/default'

Update documentation

See merge request fluiddyn/fluidsim!352

AUTHORS.md

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+# Authors
+
+Fluidsim has first been developed by
+[Pierre Augier](http://www.legi.grenoble-inp.fr/people/Pierre.Augier/) (CNRS
+researcher at [LEGI](http://www.legi.grenoble-inp.fr), Grenoble) at KTH
+(Stockholm) as a numerical code to solve fluid equations in a periodic
+two-dimensional space with pseudo-spectral methods.
+
+Fluidsim has been greatly improved during Ashwin Vishnu PhD at KTH (Stockholm).
+
+The main contributors are:
+
+- [Pierre Augier (LEGI, CNRS, UGA)](http://www.legi.grenoble-inp.fr/people/Pierre.Augier)
+- [Ashwin Vishnu (KTH)](https://www.mech.kth.se/mech/info_staff.xhtml?ID=381)
+- [Cyrille Bonamy (LEGI, CNRS, UGA)](http://www.legi.grenoble-inp.fr/web/spip.php?auteur223)
+- [Miguel Calpe Linares (LEGI, CNRS, UGA)](http://www.legi.grenoble-inp.fr/web/spip.php?auteur328)
+- [Jason Reneuve (ENS Lyon)](http://www.ens-lyon.fr/PHYSIQUE/presentation/anciens/reneuve-jason)
+- Antoine Bardant (LEGI)
+- [Vincent Labarre](https://www.researchgate.net/profile/Vincent-Labarre)
+  ([OCA](https://www.oca.eu/fr/fluid))

CHANGES.md

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+# Release notes
+
+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).
+
+% Type of changes
+
+% ---------------
+
+% Added      Added for new features.
+
+% Changed    Changed for changes in existing functionality.
+
+% Deprecated Deprecated for soon-to-be removed features.
+
+% Removed    Removed for now removed features.
+
+% Fixed      Fixed for any bug fixes.
+
+% Security   Security in case of vulnerabilities.
+
+% Unreleased_
+
+% -----------
+
+% towncrier release notes start
+
+## [0.7.4] (2023-10-05)
+
+- [!342](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/342)
+  Refactoring and improvements spectra ns2d and ns3d.
+- [!335](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/335)
+  Improvement `fluidsim-ipy-load` which can now take a path as argument
+- Code improvements, bug fixes (in particular for movies) and compatibility with
+  new Matplotlib
+
+## [0.7.3] (2023-05-24)
+
+- Official support for only Python 3.9, 3.10 and 3.11.
+- Few improvements for
+  [Fluidsimfoam](https://foss.heptapod.net/fluiddyn/fluidsimfoam).
+
+## [0.7.2] (2023-01-05)
+
+- New module {mod}`fluidsim_core.output.remaining_clock_time`.
+
+## [0.7.1] (2022-11-30)
+
+- [!325](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/325) Small
+  changes in restarts utilities for Snek5000 0.8.0.
+
+## [0.7.0] (2022-11-23)
+
+- [!316](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/316)
+  Interactive movies
+
+- [!317](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/317) and
+  [!318](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/318)
+
+  - Refactor movie code in fluidsim-core with several improvements and bugfixes
+    ({mod}`fluidsim_core.output.movies` and
+    {mod}`fluidsim_core.output.phys_fields`)
+  - Movies for Snek5000
+
+- [!319](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/319)
+  Refactor restart code in fluidsim-core
+  ({class}`fluidsim_core.scripts.restart.RestarterABC` and
+  {class}`fluidsim.util.scripts.restart.Restarter`)
+
+- [!320](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/320) Restart
+  for Snek5000 in fluidsim-core
+
+- [!321](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/321) command
+  `fluidsim-ipy-load`.
+
+## [0.6.1] (2022-09-07)
+
+- Turbulence models with `extend_simul_class`
+  ([!308](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/308), see
+  {mod}`fluidsim.base.turb_model`)
+
+- Kolmogorov forcing
+  ([!307](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/307), see
+  {mod}`fluidsim.base.forcing.kolmogorov`)
+
+- Output {mod}`fluidsim.base.output.horiz_means`
+  ([!309](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/309))
+
+- Output {mod}`fluidsim.base.output.cross_corr3d`
+  ([!295](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/295))
+
+- Better support for 3d FFT libs based on pencil decompositions
+  ([!283](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/283))
+
+- [!289](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/289)
+
+  - File `is_being_advanced.lock` in the result directory during the runs
+  - Better handling of signals (`SIGINT`, `SIGTERM` and `SIGUSR2`)
+  - `fluidsim-restart` supports idempotent jobs (OAR scheduler)
+  - {func}`fluidsim.util.get_dataframe_from_paths` using
+    `sim.output.get_mean_values`
+  - {func}`fluidsim.util.get_last_estimated_remaining_duration`
+  - `sim.output.spatiotemporal_spectra.get_spectra`
+
+- CI also running on Github Actions
+  ([!224](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/224))
+
+- Various fixes (in particular energy steps with `fluidsim-restart`)
+
+- Various plot improvements (in particular `plot_omega_emp` in
+  {mod}`fluidsim.base.output.spatiotemporal_spectra`)
+
+## [0.6.0] (2022-02-07)
+
+- New subpackage {mod}`fluidsim.util.scripts` and module
+  {mod}`fluidsim.util.scripts.turb_trandom_anisotropic`
+  ([!255](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/255)).
+
+- Entry points console_scripts `fluidsim-restart`
+  ([!261](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/261)) and
+  `fluidsim-modif-resolution`
+  ([!263](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/263)).
+
+- Forcing
+  {class}`fluidsim.base.forcing.anisotropic.TimeCorrelatedRandomPseudoSpectralAnisotropic`
+  (extension for 3d solvers + new parameter
+  `params.forcing.tcrandom_anisotropic.delta_angle`)
+  ([!247](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/247)).
+
+- New projection functions (toroidal/poloidal) in
+  {mod}`fluidsim.operators.operators3d`
+  ([!247](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/247)).
+
+- [! 250](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/250): New
+  parameter `params.projection` for ns3d solvers.
+
+  The equations (`ns3d`, `ns3d.strat` and `ns3d.bouss`) can be modified by
+  projecting the solutions on the poloidal or toroidal manifolds.
+
+- Faster loading at Python start
+  ([!264](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/264))
+
+- Various bugfixes, in particular related to restart.
+
+## [0.5.1] (2021-11-05)
+
+- [!244](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/244): Taylor
+  Green forcing for ns3d solvers
+- fluidsim-core: change order for the initialization of the parameters: Simul
+  class before the subclasses.
+
+## [0.5.0] (2021-09-29)
+
+### Added
+
+- [!200](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/200) : New
+  mechanism to easily extend a Simul class (subpackage
+  {mod}`fluidsim.extend_simul`).
+
+- [!201](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/201) :
+  Improve FluidSim Core API with a warning and a convenience function
+
+  - Warnings added when `_set_attrib` is called instead of `_set_child` by a
+    InfoSolver instance
+  - New function `iter_complete_params`
+
+- Output `spatial_means_regions_milestone.py` using {mod}`fluidsim.extend_simul`.
+
+- New options `no_vz_kz0` and `NO_KY0`.
+
+- Spatiotemporal spectra and many improvements for the temporal spectra for ns3d
+  and ns2d solvers by Jason Reneuve
+  ([!202](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/202), ...)
+
+- Better Burgers1d solvers (by Ashwin Vishnu)
+
+### Changed
+
+- [!200](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/200) :
+  (internal) {class}`fluidsim_core.info.InfoSolverCore`: `__init__` now fully
+  initializes the instance (calling the method `complete_with_classes`). New
+  keyword argument `only_root` to initialize only the root level.
+- [!211](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/211) :
+  Replace for ns2d solvers the output `frequency_spectra` (nearly not used) by the
+  newer output `temporal_spectra` written for ns3d solvers.
+
+### Fixed
+
+- Many bugfixes!
+
+## [0.4.1] (2021-02-02)
+
+Few bugfixes and
+[!192](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/192) (temporal
+spectra for ns3d solvers).
+
+## [0.4.0] (2021-01-11)
+
+- [!186](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requests/186):
+  Package split into `fluidsim-core` and `fluidsim`
+
+  - Base classes and abstract base classes defined for `params`, `info_solver`,
+    `sim`, `output` instances
+  - Entry points as a *plugin framework* to register FluidSim solvers
+
+- `base/output/print_stdout.py`: better regularity saving + method
+  `plot_clock_times`
+
+- Able to run bigger simulations (`2034x2034x384`) on the Occigen cluster (in
+  particular new function `fluidsim.modif_resolution_from_dir_memory_efficient`)
+
+## [0.3.3] (2020-10-15)
+
+- Bugfixes and optimizations (in particular for ns3d solvers)
+- Forcing WATU Coriolis and Milestone for ns3d.strat
+- pyproject.toml and isolated build
+- Timestepping using phase-shifting for dealiasing
+- Improve regularity of saving for some outputs
+
+## [0.3.2] (2019-11-14)
+
+- Bug fixes and Transonic 0.4 compatibility
+
+## [0.3.1] (2019-03-07)
+
+- Windows compatibility
+- Only Python code (stop using Cython)
+- Improvements ns2d.strat
+
+## [0.3.0] (2019-01-31)
+
+- Drop support for Python 2.7!
+- Accelerated by Transonic & Pythran (also time stepping)
+- Better setup.py (by Ashwin Vishnu)
+- Improvement ns2d.strat (by Miguel Calpe Linares)
+- Much better testing (internal, CI, compatibility pytest, coverage 87%)
+- Fix several bugs :-)
+- New function load_for_restart
+
+## [0.2.2] (2018-07-01)
+
+- Let fluidfft decides which FFT class to use (dependency fluidfft >= 0.2.4)
+
+## [0.2.1] (2018-05-24)
+
+- IPython magic commands (by Ashwin Vishnu).
+- Bugfix divergence-free flow and time_stepping in ns3d solvers.
+
+## [0.2.0] (2018-05-04)
+
+- Many bugfixes and nicer code (using the Python code formatter Black).
+- Faster ns3d solver.
+- ns2d.strat + anisotropic forcing (by Miguel Calpe Linares).
+- Nicer forcing parameters.
+
+## 0.1.1
+
+- Better `phys_fields.plot` and `phys_fields.animate` (by Ashwin Vishnu and Miguel
+  Calpe Linares).
+- Faster installation (with configuration file).
+- Installation without mpi4py.
+- Faster time stepping with less memory allocation.
+- Much faster ns3d solvers.
+
+## 0.1.0
+
+- Uses fluidfft and Pythran
+
+## 0.0.5
+
+- Compatible fluiddyn 0.1.2
+
+## 0.0.4
+
+- 0D models (predaprey, lorenz)
+- Continuous integration, unittests with bitbucket-pipelines
+
+## 0.0.3a0
+
+Merge with geofluidsim (Ashwin Vishnu Mohanan repository)
+
+- Movies.
+- Preprocessing of parameters.
+- Less bugs.
+
+## 0.0.2a1
+
+- Use a cleaner parameter container class (fluiddyn 0.0.8a1).
+
+## 0.0.2a0
+
+- SetOfVariables inherits from numpy.ndarray.
+- The creation of default parameter has been simplified and is done by a class
+  function Simul.create_default_params.
+
+## 0.0.1a
+
+- Split the package fluiddyn between one base package and specialized packages.
+
+[0.2.0]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.1.1...0.2.0
+[0.2.1]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.2.0...0.2.1
+[0.2.2]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.2.1...0.2.2
+[0.3.0]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.2.2...0.3.0
+[0.3.1]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.3.0...0.3.1
+[0.3.2]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.3.1...0.3.2
+[0.3.3]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.3.2...0.3.3
+[0.4.0]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.3.3...0.4.0
+[0.4.1]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.4.0...0.4.1
+[0.5.0]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.4.1...0.5.0
+[0.5.1]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.5.0...0.5.1
+[0.6.0]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.5.1...0.6.0
+[0.6.1]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.6.0...0.6.1
+[0.7.0]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.6.1...0.7.0
+[0.7.1]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.7.0...0.7.1
+[0.7.2]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.7.1...0.7.2
+[0.7.3]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.7.2...0.7.3
+[0.7.4]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.7.3...0.7.4