Doc: convert files to .md

AUTHORS.md

@@ -0,0 +1,20 @@
+# 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

@@ -2,10 +2,9 @@
 
 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).
+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
 
@@ -35,126 +34,146 @@ Versioning](https://semver.org/spec/v2.0.0.html).
   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
+- 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).
+- 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.
+- [!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)
+- [!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`)
+    ({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
+- [!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`.
+- [!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
+- 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
+- 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.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))
+- 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))
+- 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_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))
+- 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`)
+- 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`)
+  {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)).
+  {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.
+- [! 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))
+- 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
+- [!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
+- [!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
+  - 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), ...)
+- 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)
 
@@ -165,26 +184,30 @@ Versioning](https://semver.org/spec/v2.0.0.html).
   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.
+  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).
+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`
+- [!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
+  - 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`
+- `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`)
@@ -235,8 +258,8 @@ Few bugfixes and [!192](https://foss.heptapod.net/fluiddyn/fluidsim/-/merge_requ
 
 ## 0.1.1
 
-- Better `phys_fields.plot` and `phys_fields.animate` (by Ashwin Vishnu and
-  Miguel Calpe Linares).
+- 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.
@@ -270,13 +293,12 @@ Merge with geofluidsim (Ashwin Vishnu Mohanan repository)
 ## 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.
+- 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.
+- 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
@@ -296,4 +318,3 @@ Merge with geofluidsim (Ashwin Vishnu Mohanan repository)
 [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
-[unreleased]: https://foss.heptapod.net/fluiddyn/fluidsim/-/compare/0.7.3...branch%2Fdefault

doc/authors.md

@@ -0,0 +1 @@
+../AUTHORS.md

doc/conf.py

@@ -335,7 +335,9 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", "FluidSim", "FluidSim Documentation", ["Pierre Augier"], 1)]
+man_pages = [
+    ("index", "FluidSim", "FluidSim Documentation", ["Pierre Augier"], 1)
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -390,7 +392,7 @@
 myst_enable_extensions = [
     "amsmath",
     # "attrs_inline",
-    # "colon_fence",
+    "colon_fence",
     # "deflist",
     "dollarmath",
     # "fieldlist",

doc/examples.md

@@ -0,0 +1,18 @@
+# Examples
+
+```{toctree}
+---
+maxdepth: 2
+---
+examples/running-simul-onlineplot
+examples/running-simul-cluster
+examples/running-simul-restart
+examples/init-fields-in-script
+examples/init-fields-in-script-3d
+examples/forcing-in-script
+examples/static-layers
+ipynb/executed/taylor-green
+```
+
+There are more interesting examples in
+<https://foss.heptapod.net/fluiddyn/fluidsim/tree/branch/default/doc/examples>!