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Refactor info to allow datetime inputs from xarray.Dataset and pandas.DataFrame tables #619

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merged 7 commits into from
Sep 21, 2020

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@weiji14 weiji14 commented Sep 20, 2020

Description of proposed changes

In order to support datetime inputs into pygmt.info, this PR changes the backend mechanism from using lib.virtualfile_from_matrix() (which only supports single non-datetime dtypes) to using lib.virtualfile_from_vectors() (which supports datetime inputs as of #464).

Note: While datetime inputs can be passed into info now, the resulting outputs (UNIX timestamp instead of ISO datetime) might not make sense due to the issue at GenericMappingTools/gmt#4241.

Coincidentally, this refactor also enables the following:

Addresses #597, will be fixed once GenericMappingTools/gmt#4241 is resolved.

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.

@weiji14 weiji14 added the enhancement Improving an existing feature label Sep 20, 2020
Comment on lines +49 to +53
output = info(table=table)
expected_output = (
"<vector memory>: N = 5 <10/15> <2020-01-01T00:00:00/2020-01-05T00:00:00>\n"
)
assert output == expected_output
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@weiji14 weiji14 Sep 20, 2020

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Note that this test currently fails, giving what looks like a UNIX timestamp rather than an ISO datetime output:

E       AssertionError: assert '<vector memo...1578182400>\n' == '<vector memo...5T00:00:00>\n'
E         - <vector memory>: N = 5 <10/15> <2020-01-01T00:00:00/2020-01-05T00:00:00>
E         + <vector memory>: N = 5 <10/15> <1577836800/1578182400>

Will need to investigate, but any idea why this is happening? Or is this expected behaviour?

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GMT_Put_Vector started to accept datetime strings in PR GenericMappingTools/gmt#3396. In this implementation, all datetime strings are converted to double internally.

Looks like a GMT API bug to me.

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@weiji14 weiji14 Sep 20, 2020

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So the inputs are read correctly here, we can pass in datetime types using the GMT_DATETIME enum. The output is also the correct UNIX timestamp range, but I doubt it's something users would expect.

I suppose we can xfail this for 6.1.1, but would prefer to have this reported and/or fixed in GMT master first (i.e. for 6.2.0) Edit: issue opened at GenericMappingTools/gmt#4241. A workaround might be to use np.datetime64(1577836800, 's') to get numpy.datetime64('2020-01-01T00:00:00'), but this isn't a nice solution.

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I suppose we can xfail this for 6.1.1,

Yes to me.

@weiji14 weiji14 marked this pull request as ready for review September 21, 2020 00:05
pygmt/modules.py Outdated Show resolved Hide resolved
weiji14 and others added 2 commits September 21, 2020 12:34
@weiji14 weiji14 merged commit a4d414a into master Sep 21, 2020
@weiji14 weiji14 deleted the info_on_datetime branch September 21, 2020 01:02
weiji14 added a commit to weiji14/deepicedrain that referenced this pull request Nov 11, 2020
Bumps [pygmt](https://github.com/GenericMappingTools/pygmt) from 0.2.0 to 0.2.0+53.gc7c5e.
- [Release notes](https://github.com/GenericMappingTools/pygmt/releases)
  - [Changelog](https://github.com/GenericMappingTools/pygmt/blob/master/doc/changes.rst)
  - [Commits](GenericMappingTools/pygmt@v0.2.0...v0.2.0-53-gc7c5e)

Had to fix a broken test by using a pandas.DataFrame input to `pygmt.info` instead of a pandas.Series, because of GenericMappingTools/pygmt#619. Also pinned intake-geopandas to the v0.2.4 tag, same version, just using the wheel now.
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