Veros

This is a huge release with many exciting changes!

**This release is not backwards-compatible**. Setups created with v0.1.x will have to be rewritten to work with this version.

Changes

- Veros now fully supports distributed architectures through MPI, for both NumPy and Bohrium backends. If you have MPI installed, just run something like

bash
$ mpirun -n 4 python mysetup.py -n 2 2


to get started.

- A new realistic flexible resolution setup (`global_flexible`) that automatically adapts to the chosen resolution. Just choose a resolution and time step and that's it! Also comes with automatic removal of marginal seas.

- Better output and logging capabilities: terminal colors, a progress bar and throughput indicator, more verbosity options.

- A re-implementation of the island routines, which are now faster and more stable.

- A fully distributed Poisson solver via PETSc that is over 10x faster than PyOM's solver.

- netCDF output via HDF5, so libnetcdf is not a dependency anymore.

- The old `Veros` base class is now separated into `VerosSetup` (containing all setup-specific logic) and `VerosState` (holding the model settings and variables).

- Global runtime settings:

python
from veros import runtime_settings as rs

rs.backend = 'bohrium'


- Polished documentation.

- Various code quality improvements and polish.

Removed features

- Dropped Python 2 support.

- Removed Eady setup.

- Removed `logfile` argument.

Veros on PyPI

Veros is now installable via `pip`! This allows you to get started with Veros in lightning speed:

bash
$ pip install veros
$ veros copy-setup --to /tmp
$ python /tmp/acc/acc.py


Other changes

- Command line interfaces are now based on `click` instead of `argparse`.
- Unless explicitly told, Veros does not consume any arguments from the command line any more. In setups meant to be run interactively, you can add the following to parse command line arguments:

python
veros.tools.cli
def run(*args, **kwargs):
simulation = MySetup(*args, **kwargs)
simulation.setup()
simulation.run()


if __name__ == "__main__":
run()

- Setup assets (i.e., external binary files required to run the standard setups) are now downloaded on demand to `$HOME/.veros`, or to wherever the environment variable `VEROS_ASSET_DIR` pointed when Veros was imported.
- Git LFS is not required anymore.
- Veros is now licensed under a MIT license.

The first official release of Veros!

All core routines in this version are more or less direct (vectorized) translations of their respective pyOM 2.1.0 counterpart.

The code is optimized for use with NumPy or Bohrium, using either the OpenMP or OpenCL backend.

Supports both Python 2.7 and 3.x, but you might run into issues with Bohrium on Python 3.x.