xarray-simlab: xarray extension for computer model simulations

|Build Status| |Coverage| |Doc Status| |Zenodo|

xarray-simlab is a Python library that provides both a generic framework for building computational models in a modular fashion and a xarray_ extension for setting and running simulations using the xarray's Dataset structure. It is designed for fast, interactive and exploratory modeling.

xarray-simlab is well integrated with other libraries of the PyData ecosystem such as dask <https://docs.dask.org>_ and zarr <https://zarr.readthedocs.io>_.

.. _xarray: http://xarray.pydata.org .. |Build Status| image:: https://github.com/xarray-contrib/xarray-simlab/workflows/test/badge.svg?branch=master :target: https://github.com/xarray-contrib/xarray-simlab/actions?workflow=test :alt: Build Status .. |Coverage| image:: https://codecov.io/gh/xarray-contrib/xarray-simlab/branch/master/graphs/badge.svg?branch=master :target: https://codecov.io/github/xarray-contrib/xarray-simlab?branch=master :alt: Coverage Status .. |Doc Status| image:: http://readthedocs.org/projects/xarray-simlab/badge/?version=latest :target: http://xarray-simlab.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status .. |Zenodo| image:: https://zenodo.org/badge/93938479.svg :target: https://zenodo.org/badge/latestdoi/93938479 :alt: Citation

In a nutshell

The Conway's Game of Life example shown below is adapted from this blog post <https://jakevdp.github.io/blog/2013/08/07/conways-game-of-life/>_ by Jake VanderPlas.

1. Create new model components by writing compact Python classes, i.e., very much like dataclasses_:

.. code-block:: python

import numpy as np
import xsimlab as xs

@xs.process
class GameOfLife:
    world = xs.variable(
        dims=('x', 'y'), intent='inout', encoding={'fill_value': None}
    )

    def run_step(self):
        nbrs_count = sum(
            np.roll(np.roll(self.world, i, 0), j, 1)
            for i in (-1, 0, 1) for j in (-1, 0, 1)
            if (i != 0 or j != 0)
        )
        self._world_next = (nbrs_count == 3) | (self.world & (nbrs_count == 2))

    def finalize_step(self):
        self.world[:] = self._world_next


@xs.process
class Glider:
    pos = xs.variable(dims='point_xy', description='glider position')
    world = xs.foreign(GameOfLife, 'world', intent='out')

    def initialize(self):
        x, y = self.pos

        kernel = [[1, 0, 0],
                  [0, 1, 1],
                  [1, 1, 0]]

        self.world = np.zeros((10, 10), dtype=bool)
        self.world[x:x+3, y:y+3] = kernel

2. Create a new model just by providing a dictionary of model components:

.. code-block:: python

model = xs.Model({'gol': GameOfLife,
                  'init': Glider})

3. Create an input xarray.Dataset, run the model and get an output xarray.Dataset:

.. code-block:: python

input_dataset = xs.create_setup(
    model=model,
    clocks={'step': np.arange(9)},
    input_vars={'init__pos': ('point_xy', [4, 5])},
    output_vars={'gol__world': 'step'}
)

output_dataset = input_dataset.xsimlab.run(model=model)

.. code-block:: python

>>> output_dataset
<xarray.Dataset>
Dimensions:     (point_xy: 2, step: 9, x: 10, y: 10)
Coordinates:
  * step        (step) int64 0 1 2 3 4 5 6 7 8
Dimensions without coordinates: point_xy, x, y
Data variables:
    init__pos   (point_xy) int64 4 5
    gol__world  (step, x, y) bool False False False False ... False False False

4. Perform model setup, pre-processing, run, post-processing and visualization in a functional style, using method chaining:

.. code-block:: python

import matplotlib.pyplot as plt

with model:
    (input_dataset
     .xsimlab.update_vars(
         input_vars={'init__pos': ('point_xy', [2, 2])}
     )
     .xsimlab.run()
     .gol__world.plot.imshow(
         col='step', col_wrap=3, figsize=(5, 5),
         xticks=[], yticks=[],
         add_colorbar=False, cmap=plt.cm.binary)
    )

.. image:: doc/_static/gol.png :width: 400px

.. _dataclasses: https://docs.python.org/3/library/dataclasses.html

Documentation

Documentation is hosted on ReadTheDocs: http://xarray-simlab.readthedocs.io

License

3-clause ("Modified" or "New") BSD license, see License file <https://github.com/xarray-contrib/xarray-simlab/blob/master/LICENSE>__.

xarray-simlab uses short parts of the code of the xarray_, pandas_ and dask_ libraries. Their licenses are reproduced in the "licenses" directory.

.. _pandas: http://pandas.pydata.org/

Acknowledgment

This project is supported by the Earth Surface Process Modelling_ group of the GFZ Helmholtz Centre Potsdam.

.. _Earth Surface Process Modelling: http://www.gfz-potsdam.de/en/section/earth-surface-process-modelling/

Citation

If you use xarray-simlab in a scientific publication, we would appreciate a citation_.

.. _citation: http://xarray-simlab.readthedocs.io/en/latest/citation.html