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

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

• Donation links.

• {func}snek5000.find_configfile removes call to deprecated function.
• Explicit ValueError when no coordinates are defined and history points object's load method is invoked.
• Minor corrections in README.md and documentation and JOSS manuscript.

• New command snek-make-nek to clean and rebuild Nek5000 tools
• JOSS paper draft

Documentation

• How to use adaptive time step
• How to configure C and Fortran compilers
• Document the new copier template

• Use remaining_clock_time by default
• Replace isort and flake8 with ruff, upgrade hooks

• {mod}snek5000.output.remaining_clock_time.
• {func}snek5000.output.base.Output.post_init_create_additional_source_files, {func}snek5000.resources.get_base_templates and {func}snek5000.resources.get_base_template.
• {class}snek5000.output.spatial_means.SpatialMeans.
• New block user_size in SIZE.j2 template (see {mod}snek5000.resources).

• Functions deprecated in 0.8.0 (source_root, get_asset, get_root, get_configfile, _complete_params_from_par_file).
• Subpackage snek5000.assets.

This is the first stable version and is the result of a huge work (more than 550 commits and 60 closed issues). To summarize, we work a lot on stability, on improving the API, the logging and the user experience, and on improving our documentation and tutorials. The following lists are a very incomplete lists of the additions, changes and deprecations.

• Commands snek-make, snek-restart, snek-info, snek-ipy-load and snek-generate-config.
• Functions {func}snek5000.util.restart.load_for_restart, {func}snek5000.params.load_params
• {mod}snek5000.util.files
• {meth}snek5000.output.base.Output.get_field_file to locate a field file
• Mandatory key MPIEXEC_FLAGS in Snakemake config
• {class}snek5000.output.history_points.HistoryPoints for {ref}Nek5000 history points <nek:features_his>
• {class}snek5000.output.phys_fields.PhysFields now fully functional with load and get_var methods provided by classes under {mod}snek5000.output.readers.
• Support for number of processes detection in OAR clusters
• {meth}snek5000.output.base.Output._set_info_solver_classes to customize Output child classes
• Environment variable SNEK_UPDATE_CONFIG_ENV_SENSITIVE, {meth}snek5000.output.base.Output.write_snakemake_config to help the user easily modify environment variables during Snakemake rule execution. See {ref}override_config.

• Mandatory environment variable NEK_SOURCE_ROOT.
• params.oper.elem.staggered has a new default value auto, which sets staggered grid if a linear solver is used and a collocated one if some other solver is used. Explicitly setting params.oper.elem.staggered = True is required to maintain previous default behaviour.
• {func}snek5000.util.files.next_path gets force_suffix and return_suffix parameters
• {meth}snek5000.output.base.Output._save_info_solver_params_xml updates .par and params_simul.xml file on loading for restart
• Shorter output while executing genmap
• Field files will be stored in sessions enabling restart with symlinking of restart files and avoids clobbering existing solution files
• Support extension .usr.f to facilitate syntax highlighting and which would be copied as a .usr file upon {meth}snek5000.output.base.Output.copy
• The use of params.nek.general.user_params are replaced by a more powerful {meth}snek5000.params.Parameters._record_nek_user_params method.

• {func}snek5000.params._complete_params_from_par_file (renamed as {func}snek5000.params.complete_params_from_par_file).
• {func}snek5000.util.restart.prepare_for_restart
• Passing rules as iterables to {meth}snek5000.make.Make.exec. Pass positional parameters instead.
• {func}snek5000.source_root (renamed as {func}snek5000.get_nek_source_root).
• {meth}snek5000.output.base.Output.get_root (renamed as {meth}snek5000.output.base.Output.get_path_solver_package).
• {meth}snek5000.output.base.Output.get_configfile (use a string "config_simul.yml" instead in user Snakefile).
• The warnings parameter in {meth}snek5000.output.base.Output.update_snakemake_config is deprecated! Use verbosity=0 (now default) to disable warnings.

• Parameter warnings in {func}snek5000.util.smake.append_debug_flags is replaced by a separate function {func}snek5000.util.smake.set_compiler_verbosity.

• Detection of linear Nek5000 solvers
• Append debug flags to config, even if CFLAGS and FFLAGS are missing

• Ability to customize number of processes with {meth}snek5000.make.Make.exec
• Documentation on configuring snek5000 compilation and execution

• Use rich for logging
• No need to wait for <case>.f file which is deleted by new Nek5000 version
• {func}snek5000.load alias for {func}snek5000.load_simul which also loads from current directory when no argument is passed
• Fix {meth}snek5000.solvers.base.InfoSolver._complete_params_with_default into a classmethod (thanks @paugier)
• params.oper.max.order_time is now a property {any}snek5000.operators.Operators.max_order_time

• Rule srun renamed as called run_fg

• Allow name_solver to be different from the "package name" (thanks @paugier)

• {meth}update_snakemake_config and {func}append_debug_flags has a new parameter to optionally suppress compiler warnings during debug.
• Keyword arguments to pass optional template variables via write_... methods which render templates for .box, SIZE and makefile_usr.inc files.

• Remove underflow from debug flags

• Tutorial and Snakemake workflows for packaging user code, see {ref}packaging
• Module {mod}snek5000.util.smake with helper utilities to set env, flags etc.

• Much less boilerplate code for user code!
• Updated pre-commit hooks for development

• Function {func}snek5000.util.activate_paths

• Unused Snakemake rules from the top project level

• Support for 2D solvers and temp / scalar boundary conditions in Operators class.
• Attribute sim.output.params points to params.output as in FluidSim

• Nek parameter filter_modes for HPFRT and write_to_field_file
• Function load_simul to load simulations from a directory.

• Depend on fluidsim-core instead of fluidsim
• Parameters, entry points and magic implementation from fluidsim-core (#15)
• Output class now conforms to fluidsim-core API. File params.xml renamed to params_simul.xml (#16)

• Rewrite README and docs for better onboarding

• Support for Python 3.6.x
• Support for FluidSim 0.3.3
• Descriptive error messages when class Output cannot resolve resources

• Parameters for specifying mesh origin and ratio
• Coverage tests

• Support for Nek5000 v19
• Cluster's default project

• Activate $PATH logic, added tests
• No error raised by prepare_for_restart after unlock
• Bug fixes while archiving: choosing paths of new tarball

• More assets: templates, default snakemake config

• Source root path expands ~ and environment variables

• Sub-package assets and module output.base
• Helper functions source_root and get_asset

• Separate framework from the code and rename it to snek5000
• Documentation and readme to reflect the package

• ABL source code

• Pre-commit: black, flake8, isort fixing and linting support
• Jupyterlab and ipykernel configuration snakemake rules
• Job management script - organize.py
• New module: const

• Parameters for Maronga case
• Compilation is now parallel
• Two-step archival, tar and compress

• Snakemake: gslib dependency before compiling
• Snakemake: Tee output to log file

• Requirements files produced using pip-tools

• Tar shell functions in activate script
• Module snek5000.clusters for job submission

• Conda environment packages
• Reduced pressure residual tolerance for divergence check

• Bugfixes for simulation parameter loading, restart
• Snakefile dependencies for running a simulation

• KTH toolbox
• Coriolis force
• Job submission in cluster
• More user_params

• Archives use zstd compression
• user_params is a dictionary

• Initial condition bug in setting velocities in useric
• Cs - Cs**2 in eddy_visc
• Assert exit code of snakemake results in tests
• Subroutine set_forcing uses ux.. instead of vx

• Templates in abl.templates subpackage
• Expand parameters and write methods in class Operators
• Improved tests and documentation
• Solver abl respects parameters and writes box and SIZE files.

• Snakecase for nek parameters

• Uses fluidsim framework for creating a scripting layer
• Package abl with a single module and an abl.Output class
• New sub-packages and modules under snek5000: solvers, output, info, log, make, magic, operators
• Testing with pytest, and CI on GitHub actions
• Detailed documentation
• Versioning with setuptools_scm

• Extra requirements [test] renamed to [tests]
• Rename case files 3D_ABL -> abl and directory abl_nek5000 -> abl
• Overall reorganization of modules and Snakemake + configuration files.

• Scripting for managing run parameters snek5000.params
• Python packaging
• Sphinx + Doxygen + Breathe documentation