Raise GMTInvalidInput exception when required z is missing #1478

yohaimagen · 2021-09-01T05:49:55Z

adding an additional if statement to the data_kind utils function that is based on a new parameter requierd_z and checks if z vector is provided alongside x and y.

Fixes #1447

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yohaimagen · 2021-09-01T06:02:06Z

Where should I add tests for not providing the z vector?

maxrjones · 2021-09-01T20:52:28Z

Where should I add tests for not providing the z vector?

I think the test should go in pygmt/tests/test_clib.py.

yohaimagen · 2021-09-02T06:25:53Z

I added the test.

If we decide to go the route of requierd_z(see discussion at #1447) we should add requierd_z = True in all the functions that do require z column. Should we do it over here or in a separate PR for each function?

maxrjones

I recommend adding required_z to the appropriate functions in this PR.

It would be good to raise the same exception if the data kind is matrix (L78) and data.shape[1] < 3 when required_z is set. Would you be able to add this to the PR and add another pytest.raises(GMTInvalidInput) check to the new test?

pygmt/helpers/utils.py

Co-authored-by: Meghan Jones <meghanj@alum.mit.edu>

yohaimagen · 2021-09-03T10:37:48Z

/format

yohaimagen · 2021-09-03T11:11:00Z

I am making a list of functions that should pass required_z=True please add functions that I've missed. There are quite a lot of new functions that have been wrapped recently and will be released in 0.5 please let me know which one of them needs to be set required_z=True.

yohaimagen · 2021-09-03T11:36:51Z

Should we remove the tests of the relevant functions that test the passing of z column?

pygmt/pygmt/tests/test_contour.py

Lines 42 to 56 in cd822ca

    
           for variable in product([None, data[:, 0]], repeat=3): 
        
               # Filter one valid configuration: 
        
               if not any(item is None for item in variable): 
        
                   continue 
        
               with pytest.raises(GMTInvalidInput): 
        
                   fig.contour( 
        
                       x=variable[0], 
        
                       y=variable[1], 
        
                       z=variable[2], 
        
                       region=region, 
        
                       projection="X4i", 
        
                       color="red", 
        
                       frame="afg", 
        
                       pen="", 
        
                   )

if so we shuld extend the test to be similar to the above.

maxrjones

Nice work, thank you! 🎉

As you have seen, we leave approved pull requests up for at least a day so other maintainers have a final opportunity to check it out. In the meantime, please apply the two minor grammatical suggestions.

pygmt/tests/test_clib.py

Co-authored-by: Meghan Jones <meghanj@alum.mit.edu>

yohaimagen · 2021-09-14T05:06:14Z

Actually, when writing the test for the case of a 2d array data with less than three columns when z is required, I noticed that we do not check that 2d array data have at least 2 columns in the general case, should we raise an error if a 2d matrix of a shape nx1 is passed? and if so should I add it here or open another PR?

pygmt/tests/test_clib.py

seisman · 2021-09-14T06:35:32Z

Actually, when writing the test for the case of a 2d array data with less than three columns when z is required, I noticed that we do not check that 2d array data have at least 2 columns in the general case, should we raise an error if a 2d matrix of a shape nx1 is passed? and if so should I add it here or open another PR?

It's more complicated, because for some modules (e.g., histogram), only one column is required.

Co-authored-by: Dongdong Tian <seisman.info@gmail.com>

seisman · 2021-09-14T23:04:10Z

Actually, when writing the test for the case of a 2d array data with less than three columns when z is required, I noticed that we do not check that 2d array data have at least 2 columns in the general case, should we raise an error if a 2d matrix of a shape nx1 is passed? and if so should I add it here or open another PR?

It's more complicated, because for some modules (e.g., histogram), only one column is required.

I think this PR is good for merge and we can deal with the 2-column data check in another issue/PR.

maxrjones

I agree with @seisman that more changes aren't needed. Great work, thanks!

Following GenericMappingTools#1478.

weiji14 · 2021-09-18T22:27:39Z

pygmt/helpers/utils.py

@@ -78,6 +80,8 @@ def data_kind(data, x=None, y=None, z=None):
    elif hasattr(data, "__geo_interface__"):
        kind = "geojson"
    elif data is not None:
+        if required_z and data.shape[1] < 3:


Checking for data.shape[1] fails for xarray.Dataset inputs with AttributeError: 'Dataset' object has no attribute 'shape'. The shape attribute is valid only for numpy.ndarray, pandas.DataFrame, and maybe a few other PyData objects. Will need to create a bugfix and add some extra tests for xarray.Dataset inputs.

I can submit a PR fix since I think that I suggested this. But I feel that we should not label it as a bug since this code has not yet been included in a release, so it might be confusing to list on the changelog as a bugfix relative to v0.4.1.

Edit: Just noticed the comment on the other PR that @weiji14 would fix this. That's also fine.

Ok, I've submitted a bugfix PR at #1523. Have put on the skip-changelog label so it won't show up in the changelog :)

…ppingTools#1478) Co-authored-by: Meghan Jones <meghanj@alum.mit.edu> Co-authored-by: Dongdong Tian <seisman.info@gmail.com>

yohaimagen added 2 commits September 1, 2021 08:37

add required_z parameters, and if statement to handle missing z vector

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add required_z parameters and pass it to data_kind

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yohaimagen added the enhancement Improving an existing feature label Sep 1, 2021

yohaimagen self-assigned this Sep 1, 2021

test requierd_z

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Update pygmt/helpers/utils.py

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checks that when required z data matrix has at least 3 columns

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[format-command] fixes

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add required_z=True to _blockm

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add required_z=True to contour

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add required_z=True to plot3d

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add required_z=True to surface

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Merge branch 'main' into raise_GMTInvalidInput_exception_when_z_missing

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seisman changed the title ~~Raise gmt invalid input exception when z missing~~ Raise GMTInvalidInput exception when z missing Sep 14, 2021

seisman changed the title ~~Raise GMTInvalidInput exception when z missing~~ Raise GMTInvalidInput exception when required z is missing Sep 14, 2021

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Merge branch 'main' into raise_GMTInvalidInput_exception_when_z_missing

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weiji14 added a commit to JamieJQuinn/pygmt that referenced this pull request Sep 16, 2021

Remove test_nearneighbor_input_xy_no_z

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Following GenericMappingTools#1478.

seisman mentioned this pull request Sep 18, 2021

Wrap nearneighbor #1379

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weiji14 mentioned this pull request Sep 19, 2021

Let required_z check work on xarray.Dataset inputs #1523

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sixy6e pushed a commit to sixy6e/pygmt that referenced this pull request Dec 21, 2022

Raise GMTInvalidInput exception when required z is missing (GenericMa…

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…ppingTools#1478) Co-authored-by: Meghan Jones <meghanj@alum.mit.edu> Co-authored-by: Dongdong Tian <seisman.info@gmail.com>

weiji14 mentioned this pull request Jul 5, 2023

Add private function _validate_data_input to validate input data #2595

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Raise GMTInvalidInput exception when required z is missing #1478

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Raise GMTInvalidInput exception when required z is missing #1478

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