Wrap grdfill

[willschlitzer]

This pull request wraps the grdfill module.

Fixes #

Reminders

• Run make format and make check to make sure the code follows the style guide.
• Add tests for new features or tests that would have caught the bug that you're fixing.
• Add new public functions/methods/classes to doc/api/index.rst.
• Write detailed docstrings for all functions/methods.
• If adding new functionality, add an example to docstrings or tutorials.

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[willschlitzer]

@GenericMappingTools/pygmt-contributors Any ideas for how to test this? I have downloaded grid files from scientific cruises to ensure I have gaps in the data that need to be filled, but I'm not sure how to write a test that retrieves an unfilled grid from something like pygmt.datasets.

[maxrjones]

@GenericMappingTools/pygmt-contributors Any ideas for how to test this? I have downloaded grid files from scientific cruises to ensure I have gaps in the data that need to be filled, but I'm not sure how to write a test that retrieves an unfilled grid from something like pygmt.datasets.

You can manual set one or more of the data values in grids from pygmt.datasets to NaN to test the result from grdfill. For example:

import numpy as np
import pytest
import xarray as xr
from pygmt import grdfill
from pygmt.datasets import load_earth_relief


@pytest.fixture(scope="module", name="grid")
def fixture_grid():
    """
    Load the grid data from the sample earth_relief file and set value(s) to NaN.
    """
    grid = load_earth_relief(registration="pixel")
    grid[10,10] = np.nan
    return grid

def test_grdfilter_dataarray_in_dataarray_out(grid):
    """
    grdfill an input DataArray, and output as DataArray.
    """
    result = grdfill(grid=grid,mode="c20")
    # check information of the output grid
    assert isinstance(result, xr.DataArray)
    assert result[10,10] == 20

[willschlitzer]

You can manual set one or more of the data values in grids from pygmt.datasets to NaN to test the result from grdfill. For example:

Thanks @meghanrjones!

[seisman]

Looks good to me.

[michaelgrund]

Looks good to me. Great work!

[core-man]

Looks great. Only two minor comments.

[core-man]

LaTeX formula?

Suggested change

	pixels [default radius is `r^2 = sqrt(X^2 + Y^2)`,
	pixels [default radius is :math:`r^2 = \sqrt{X^2 + Y^2}`,

[seisman]

If you want to use the math directive, it should be:

:math:`r^2 = \sqrt{X^2 + Y^2}`

[core-man]

If you want to use the math directive, it should be:

:math:`r^2 = \sqrt{X^2 + Y^2}`

updated~ Thanks

[maxrjones]

@willschlitzer previously had this in there - it did not work because fmt_docstring tries to insert common text into the brackets. So, it either needs to stay as non-sphinx math or fmt_docstring needs to be modified.

[seisman]

If we want LaTeX math, we may need to use double curly braces

:math:`r^2 = \sqrt{{ X^2 + Y^2 }}`

See https://stackoverflow.com/questions/5466451

[willschlitzer]

If we want LaTeX math, we may need to use double curly braces

:math:`r^2 = \sqrt{{ X^2 + Y^2 }}`

See https://stackoverflow.com/questions/5466451

This appears to be working!

[maxrjones]

What is the preferred was for denoting required parameters? I think there should be some indication in the method docs that mode (-A) is required.

[weiji14]

Just some suggestions to improve the unit tests (smaller grid for speed + more robust checks) 😁 I've also thrown in some np.inf values just to see if GMT would fill them in.

What is the preferred was for denoting required parameters? I think there should be some indication in the method docs that mode (-A) is required.

Perhaps just a one-line description in the docstring wll suffice?