grdtrack: Fix the bug when profile is given

[seisman]

Description of proposed changes

Fixes #1827.

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 wrapping a new module, open a 'Wrap new GMT module' issue and submit reasonably-sized PRs.
• If adding new functionality, add an example to docstrings or tutorials.

Slash Commands

You can write slash commands (/command) in the first line of a comment to perform
specific operations. Supported slash commands are:

• /format: automatically format and lint the code
• /test-gmt-dev: run full tests on the latest GMT development version

[weiji14]

Does pygmt.which work with local NetCDF files? Also, not sure if I like this if-condition that requires opening a file using xr.open_dataarray to check if it is a grid. What about using grdinfo instead?

[seisman]

Does pygmt.which work with local NetCDF files?

Yes, it works.

Also, not sure if I like this if-condition that requires opening a file using xr.open_dataarray to check if it is a grid. What about using grdinfo instead?

grdinfo doesn't work. We don't catch the errors when reading a non-grid file:

pygmt.grdinfo("pygmt/tests/data/points.txt")
grdinfo (gmtapi_import_grid): Not a supported grid format [pygmt/tests/data/points.txt]
[Session pygmt-session (2)]: Error returned from GMT API: GMT_GRID_READ_ERROR (18)
[Session pygmt-session (2)]: Error returned from GMT API: GMT_GRID_READ_ERROR (18)

[weiji14]

Hmm, so pygmt.grdinfo produces a blank string for non-grid files. What about a check like:

if pygmt.grdinfo(grid) != "":
    is_a_grid = True
else:
    is_a_grid = False

As an aside, we colud also think about making grdinfo produce proper Python errors as part of the grdinfo refactor (#593).

[seisman]

if pygmt.grdinfo(grid) != "":
    is_a_grid = True
else:
    is_a_grid = False

It may work, but users will see the errors like:

grdinfo (gmtapi_import_grid): Not a supported grid format [pygmt/tests/data/points.txt]
[Session pygmt-session (2)]: Error returned from GMT API: GMT_GRID_READ_ERROR (18)
[Session pygmt-session (2)]: Error returned from GMT API: GMT_GRID_READ_ERROR (18)

[weiji14]

Hmm yeah, I tried pygmt.grdinfo(grid="pygmt/tests/data/points.txt", verbose="q") which removed the first error line, but still getting two [Session pygmt-session (2)]: Error returned from GMT API: GMT_GRID_READ_ERROR (18) errors printed.

[seisman]

FYI, I've changed the line to

xr.open_dataarray(which(grid, download="a")).close()

to recycle any related resources.

[weiji14]

Need a unit test to cover this line?

[seisman]

I added this unit test to cover this, but it's unclear to me why the coverage report says this line is not covered.

def test_grdtrack_set_points_and_profile(dataarray, dataframe):
    """
    Run grdtrack but set both 'points' and 'profile'.
    """
    with pytest.raises(GMTInvalidInput):
        grdtrack(grid=dataarray, points=dataframe, profile="BL/TR")

[weiji14]

I tried running that line grdtrack(grid=dataarray, points=dataframe, profile="BL/TR") and got GMTInvalidInput: Please pass in a str to 'newcolname'. So maybe move these two lines a few lines above. See my suggested change at #1867 (comment)

[weiji14]

I tried running that line grdtrack(grid=dataarray, points=dataframe, profile="BL/TR") and got GMTInvalidInput: Please pass in a str to 'newcolname'. So maybe move these two lines a few lines above. See my suggested change at #1867 (comment)

[weiji14]

Should be ok if all tests pass.