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Format .md with mdformat and execution timeout
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@paugier
paugier committed Oct 21, 2022
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137 changes: 81 additions & 56 deletions CHANGELOG.md
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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).

<!--
Expand Down Expand Up @@ -32,47 +32,51 @@ Security in case of vulnerabilities.

### Added

- Functions {func}`snek5000.util.restart.load_for_restart`, {func}`snek5000.params.load_params`
- 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`.
- {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
- {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
{meth}`snek5000.output.base.Output.write_snakemake_config` to help the user easily
modify environment variables during Snakemake rule execution. See
{ref}`override_config`.

### Changed

- `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.
- `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
- {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`
- 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.

### Deprecated

- {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`).
- 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).
- {meth}`snek5000.output.base.Output.get_configfile` (use a string `"config_simul.yml"`
instead in user Snakefile).

### Fixed

Expand All @@ -90,26 +94,29 @@ Security in case of vulnerabilities.

- 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`
- {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`

### Removed

- Rule `srun` renamed as called `run_fg`

### Fixed

- Allow ``name_solver`` to be different from the "package name" (thanks [@paugier])
- Allow `name_solver` to be different from the "package name" (thanks [@paugier])

## [0.6.1b0] - 2021-05-18

### Changed

- {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.
- {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.

### Fixed

Expand Down Expand Up @@ -151,42 +158,49 @@ Security in case of vulnerabilities.

- 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)
- Output class now conforms to `fluidsim-core` API. File `params.xml` renamed to
`params_simul.xml` (#16)

## [0.4.1b1] - 2020-10-26

### Changed
* Rewrite README and docs for better onboarding

- Rewrite README and docs for better onboarding

## [0.4.1b0] - 2020-10-26

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

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

## [0.4.0b1] - 2020-07-15

### Added

- Parameters for specifying mesh origin and ratio
- Coverage tests

### Changed

- Support for Nek5000 v19
- Cluster's default project

### Fixed

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

## [0.3.1a0] - 2020-05-10

### Added

- More assets: templates, default snakemake config

### Fixed

- Source root path expands ~ and environment variables

## [0.3.0a0] - 2020-05-09
Expand Down Expand Up @@ -232,83 +246,94 @@ Security in case of vulnerabilities.
## [0.2.1] - 2020-04-14

### Added

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

### Changed

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

### Fixed

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

## [0.2.0] - 2020-03-22

### Added

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

### Changed

- Archives use zstd compression
- user_params is a dictionary

### Fixed

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

## [0.1.1] - 2020-01-27

### Added

- 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.

### Changed

- Snakecase for `nek` parameters

## [0.1.0] - 2020-01-23

### Added

- 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`
- 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`

### Changed

- 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.

## [0.0.1] - 2020-01-17

### Added

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

[Unreleased]: https://github.com/snek5000/snek5000/compare/0.7.0b0...HEAD
[0.7.0b0]: https://github.com/snek5000/snek5000/compare/0.6.1b0...0.7.0b0
[0.6.1b0]: https://github.com/snek5000/snek5000/compare/0.6.0b0...0.6.1b0
[0.6.0b0]: https://github.com/snek5000/snek5000/compare/0.5.0b0...0.6.0b0
[0.5.0b0]: https://github.com/snek5000/snek5000/compare/0.4.1b1...0.5.0b0
[0.4.1b1]: https://github.com/snek5000/snek5000/compare/0.4.1b0...0.4.1b1
[0.4.1b0]: https://github.com/snek5000/snek5000/compare/0.4.0b1...0.4.1b0
[0.4.0b1]: https://github.com/snek5000/snek5000/compare/0.3.1a0...0.4.0b1
[0.3.1a0]: https://github.com/snek5000/snek5000/compare/0.3.0a0...0.3.1a0
[0.3.0a0]: https://github.com/snek5000/snek5000/compare/0.2.2...0.3.0a0
[0.2.2]: https://github.com/snek5000/snek5000/compare/0.2.1...0.2.2
[0.2.1]: https://github.com/snek5000/snek5000/compare/0.2.0...0.2.1
[0.2.0]: https://github.com/snek5000/snek5000/compare/0.1.1...0.2.0
[0.1.1]: https://github.com/snek5000/snek5000/compare/0.1.0...0.1.1
[0.1.0]: https://github.com/snek5000/snek5000/compare/0.0.1...0.1.0
[0.0.1]: https://github.com/snek5000/snek5000/releases/tag/0.0.1
[0.1.0]: https://github.com/snek5000/snek5000/compare/0.0.1...0.1.0
[0.1.1]: https://github.com/snek5000/snek5000/compare/0.1.0...0.1.1
[0.2.0]: https://github.com/snek5000/snek5000/compare/0.1.1...0.2.0
[0.2.1]: https://github.com/snek5000/snek5000/compare/0.2.0...0.2.1
[0.2.2]: https://github.com/snek5000/snek5000/compare/0.2.1...0.2.2
[0.3.0a0]: https://github.com/snek5000/snek5000/compare/0.2.2...0.3.0a0
[0.3.1a0]: https://github.com/snek5000/snek5000/compare/0.3.0a0...0.3.1a0
[0.4.0b1]: https://github.com/snek5000/snek5000/compare/0.3.1a0...0.4.0b1
[0.4.1b0]: https://github.com/snek5000/snek5000/compare/0.4.0b1...0.4.1b0
[0.4.1b1]: https://github.com/snek5000/snek5000/compare/0.4.1b0...0.4.1b1
[0.5.0b0]: https://github.com/snek5000/snek5000/compare/0.4.1b1...0.5.0b0
[0.6.0b0]: https://github.com/snek5000/snek5000/compare/0.5.0b0...0.6.0b0
[0.6.1b0]: https://github.com/snek5000/snek5000/compare/0.6.0b0...0.6.1b0
[0.7.0b0]: https://github.com/snek5000/snek5000/compare/0.6.1b0...0.7.0b0
[@paugier]: https://github.com/paugier
[unreleased]: https://github.com/snek5000/snek5000/compare/0.7.0b0...HEAD
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