Refactor pygmt.surface tests

[maxrjones]

Description of proposed changes

This PR captures the warnings from using short aliases in the surface test, in order to test that the warnings are generated properly and to reduce dilution of the useful information in the pytest reports.

Fixes #1460

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.

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

[willschlitzer]

@GenericMappingTools/pygmt-maintainers Are we waiting on the changes for preprocessed data as mentioned in this comment above? Or should we approve this after a decision is made on how to check the values in the returned array? If we are waiting on both changes, I suspect it won't be done by Friday.

[maxrjones]

@GenericMappingTools/pygmt-maintainers Are we waiting on the changes for preprocessed data as mentioned in this comment above? Or should we approve this after a decision is made on how to check the values in the returned array? If we are waiting on both changes, I suspect it won't be done by Friday.

I can make both changes for v0.6.0.

[weiji14]

I still see warnings in the log at https://github.com/GenericMappingTools/pygmt/runs/4109194553?check_suite_focus=true#step:11:624 😅:

___________________________ test_surface_input_file ____________________________
----------------------------- Captured stderr call -----------------------------
Warning: WARNING]: 1 unusable points were supplied; these will be ignored.
Warning: WARNING]: You should have pre-processed the data with block-mean, -median, or -mode.
Warning: WARNING]: Check that previous processing steps write results with enough decimals.
Warning: WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.
________________________ test_surface_input_data_array _________________________
----------------------------- Captured stderr call -----------------------------
Warning: WARNING]: 1 unusable points were supplied; these will be ignored.
Warning: WARNING]: You should have pre-processed the data with block-mean, -median, or -mode.
Warning: WARNING]: Check that previous processing steps write results with enough decimals.
Warning: WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.
____________________________ test_surface_input_xyz ____________________________
----------------------------- Captured stderr call -----------------------------
Warning: WARNING]: 1 unusable points were supplied; these will be ignored.
Warning: WARNING]: You should have pre-processed the data with block-mean, -median, or -mode.
Warning: WARNING]: Check that previous processing steps write results with enough decimals.
Warning: WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.
_______________________ test_surface_with_outgrid_param ________________________
----------------------------- Captured stderr call -----------------------------
Warning: WARNING]: 1 unusable points were supplied; these will be ignored.
Warning: WARNING]: You should have pre-processed the data with block-mean, -median, or -mode.
Warning: WARNING]: Check that previous processing steps write results with enough decimals.
Warning: WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.
__________________ test_surface_deprecate_outfile_to_outgrid ___________________
----------------------------- Captured stderr call -----------------------------
Warning: WARNING]: 1 unusable points were supplied; these will be ignored.
Warning: WARNING]: You should have pre-processed the data with block-mean, -median, or -mode.
Warning: WARNING]: Check that previous processing steps write results with enough decimals.
Warning: WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.

[maxrjones]

Warning: WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.

Yes this is the IEEE rounding problem because the data are not high precision, whereas the previous tests had warnings due to a lack of preprocessing. I suggest we just use verbose="e"

[weiji14]

Warning: WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.

Yes this is the IEEE rounding problem because the data are not high precision, whereas the previous tests had warnings due to a lack of preprocessing. I suggest we just use verbose="e"

I see. Or maybe we could play around with a different spacing (e.g. 1.5, 2, 2.5) and see if that works?

[maxrjones]

Warning: WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.

Yes this is the IEEE rounding problem because the data are not high precision, whereas the previous tests had warnings due to a lack of preprocessing. I suggest we just use verbose="e"

I see. Or maybe we could play around with a different spacing (e.g. 1.5, 2, 2.5) and see if that works?

If you think only reporting errors using verbose="e" is a bad idea, I can play around with the spacing and region. But, it would involve more than just changing the code in pygmt/test/test_surface.py since the current region and spacing were already used to generate the new file on the GMT server. Not that big of a deal, but I don't want to spend too much more effort here if it's not needed.

[weiji14]

Warning: WARNING]: Possibly some data were half-way between nodes and subject to IEEE 754 rounding.

Yes this is the IEEE rounding problem because the data are not high precision, whereas the previous tests had warnings due to a lack of preprocessing. I suggest we just use verbose="e"
I see. Or maybe we could play around with a different spacing (e.g. 1.5, 2, 2.5) and see if that works?

If you think only reporting errors using verbose="e" is a bad idea, I can play around with the spacing and region. But, it would involve more than just changing the code in pygmt/test/test_surface.py since the current region and spacing were already used to generate the new file on the GMT server. Not that big of a deal, but I don't want to spend too much more effort here if it's not needed.

I think your time is more valuable elsewhere, so let's just go with verbose="e" then.